I have a different problem. My application shortcuts and widgets get deleted from the desktop / home screen. One specific application that I use at least 3 to 4 times a day gets its icon deleted and the application itself gets disabled. This happens every few days. I am using Nova Launcher. I have even tried locking the Desktop to no avail.

You can check the apps 'ON' in the Security > Permissions > Autostart. Those apps which are turned on will not be killed even if you clean the RAM through Cleaner. Hope that solves your problem. Works well with me in my MIUI 7.3.6.0 Global Stable ROM. You are welcome!! :)

I confirm this problem, even in the latest verdion of MIUI8. An app like Notifocations Toggle is removed from background when closing it, even as the app is explicitly excluded from battery optimalisation.